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Author SHA1 Message Date
James A. Fellows Yates
8fff741f85
Merge branch 'dev' into nf-core-template-merge-2.5.1 2022-09-01 16:26:45 +02:00
nf-core-bot
28045430d1 Template update for nf-core/tools version 2.5.1 2022-09-01 13:34:04 +00:00
James A. Fellows Yates
2ca837a4a3
Merge pull request #115 from nf-core/json-schema 
Add documentation for all parameters JSON schema (and other minor usage documentation tweaks)
 2022-08-31 15:19:07 +02:00
James Fellows Yates
3eb136ec3c Merge branch 'dev' into json-schema 2022-08-31 12:55:49 +02:00
James A. Fellows Yates
f7b7fd63a4
Merge pull request #114 from nf-core/nf-core-template-merge-2.5 
Important! Template update for nf-core/tools v2.5
 2022-08-31 10:28:14 +02:00
James A. Fellows Yates
394084a31b
Merge pull request #113 from nf-core/filtlong-in-tests 
Improve longread QC parameters
 2022-08-31 09:36:12 +02:00
James A. Fellows Yates
5274ac57af
Update .prettierignore 2022-08-31 09:24:24 +02:00
James A. Fellows Yates
28d8d3f8fb
Merge branch 'dev' into nf-core-template-merge-2.5 2022-08-31 09:16:34 +02:00
James Fellows Yates
0107330d92 Clarify specifying output parameters in database db_params column 2022-08-31 08:34:57 +02:00
James Fellows Yates
806208c4b1 Final tweaks to schema, and add a couple of notes for dev guidance on where their various --save_reads parameters are injected 2022-08-31 08:30:26 +02:00
James Fellows Yates
acd0570b4a Finalise first pass of nextflow json documentation 2022-08-31 07:56:39 +02:00
James Fellows Yates
bdcae4f934 More docs and tweat to usage.md 2022-08-30 16:04:05 +02:00
nf-core-bot
6dfca81761 Template update for nf-core/tools version 2.5 2022-08-30 13:43:03 +00:00
James Fellows Yates
c2eaa3f6b0 Prettier 2022-08-30 14:33:40 +02:00
James Fellows Yates
d19a473c59 Merge branch 'filtlong-in-tests' into json-schema 2022-08-30 14:33:19 +02:00
James A. Fellows Yates
f393d1fe91
Update nextflow.config 2022-08-30 14:21:20 +02:00
James Fellows Yates
5552c264b9 Remove now unnecessary input validation 2022-08-30 14:14:01 +02:00
James Fellows Yates
8917e29e35 Fix accidental overly zelous search-and-replace 2022-08-30 14:11:48 +02:00
James Fellows Yates
3f8f32cba8 Make longread quality ftilering opt out 2022-08-30 14:08:05 +02:00
James Fellows Yates
afba604e8b Make everything within opt-out, once QC is opted-in 2022-08-30 14:04:34 +02:00
James Fellows Yates
95ad380173 Turn of length filtering by default for short read (to match opt in for longread qc) 2022-08-30 14:01:52 +02:00
James Fellows Yates
2cc07183a0 Standardise QC parameter system and turn on both porechop/filtlong in tests 2022-08-30 13:58:58 +02:00
James Fellows Yates
d4af88e3ff Make kaiju parameter clearer for documentation purpses and update documentation 2022-08-25 15:50:28 +02:00
James Fellows Yates
d6d51e0e43 Start work on reordering json schema parameters 2022-08-24 15:23:51 +02:00
James A. Fellows Yates
1821496a49
Merge pull request #90 from nf-core/samplesheet-check-improvement 
Make check_samplesheet.py compatible with nf-core/fetchngs
 2022-08-23 15:57:59 +01:00
James A. Fellows Yates
22e03e73e3
Merge pull request #111 from nf-core/minimal-test 
Add test_nothing config profile for very minimal testing
 2022-08-23 15:57:52 +01:00
James A. Fellows Yates
a3055bf6da
Update conf/test_nothing.config 2022-08-23 15:48:02 +02:00
James A. Fellows Yates
4315141c5f
Update bin/check_samplesheet.py 
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
 2022-08-23 15:44:53 +02:00
James Fellows Yates
e6c7939305 Add test_nothing config profile for minimal testing 2022-08-23 14:37:01 +02:00
James Fellows Yates
a97bb69cd2 Prettier 2022-08-23 14:24:57 +02:00
James A. Fellows Yates
de70b0a01d
Merge pull request #109 from nf-core/centrifuge_mqc 
Trying to get Centrifuge output into MQC
 2022-07-29 13:36:25 +02:00
James A. Fellows Yates
3e24f491b5
Merge pull request #106 from nf-core/porechop-log 
Add emitting porechop logs to multiqc and fix collection of others
 2022-07-29 10:58:12 +02:00
James A. Fellows Yates
f48b22d615
Apply suggestions from code review 2022-07-29 09:52:49 +02:00
James Fellows Yates
873a13e028 Merge remote-tracking branch 'origin/dev' into porechop-log 2022-07-29 09:51:34 +02:00
Mahwash Jamy
06298e867c
Merge pull request #105 from genomic-medicine-sweden/diamond-update 
Update the dev branch with the DIAMOND module update
 2022-07-28 17:21:59 +02:00
mjamy
5cdf5e958a Updated modules.config to add 'log' in diamond config 2022-07-28 16:08:15 +02:00
Mahwash Jamy
49487593e2
Merge branch 'nf-core:dev' into diamond-update 2022-07-28 15:48:59 +02:00
Sofia Stamouli
ba928af5ab
Merge pull request #110 from genomic-medicine-sweden/update_centrifuge_kreport 
Update centrifuge kreport
 2022-07-28 10:36:30 +02:00
sofstam
71cf32cc6a Add error strategy for centrifuge/kreport 2022-07-28 08:54:32 +02:00
sofstam
9bc45a3f24 Update centrifuge/kreport 2022-07-27 14:44:26 +02:00
sofstam
cecbb41f88 Update centrifuge/kreport 2022-07-27 14:42:35 +02:00
James Fellows Yates
25bcc0798d Start work on multiQC config with distinguishing Kraken/Centrifuge 2022-07-27 14:40:17 +02:00
nf-core-bot
a3bcf8665a [automated] Fix linting with Prettier 2022-07-26 18:47:40 +00:00
James A. Fellows Yates
65ae82efc4 Define separte krakena nd centrigfue modules 2022-07-26 18:37:33 +00:00
James A. Fellows Yates
9d2be68fb8 Merge branch 'dev' into centrifuge_mqc 2022-07-26 18:01:30 +00:00
James A. Fellows Yates
1ef0975736 Merge branch 'dev' into porechop-log 2022-07-26 18:00:28 +00:00
James A. Fellows Yates
fdd9a3bc4d
Merge pull request #107 from nf-core/fix-multiqc-mixing 
Fix MultiQC mixing
 2022-07-26 12:38:52 +02:00
James A. Fellows Yates
65b0af9a8b Fix profiling channels 2022-07-26 08:53:43 +00:00
James A. Fellows Yates
3054dea7c2 Get multiqc input working 2022-07-26 08:41:06 +00:00
James A. Fellows Yates
e76b299705 Start working getting kraken and centrifuge working in MQC 2022-07-26 08:18:54 +00:00